Flow cytometry assay methods

ABSTRACT

This document provides methods and materials involved in performing flow cytometry assay methods. For example, flow cytometry assay methods and kits are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.14/264,286, filed Apr. 29, 2014, which claims the benefit of U.S.Provisional Application Ser. No. 61/817,195, filed Apr. 29, 2013. Thedisclosures of the prior applications are considered part of (and areincorporated by reference in) the disclosure of this application.

BACKGROUND 1. Technical Field

This document relates to methods and materials involved in performingflow cytometry assay methods. For example, this document relates tomethods and materials for using flow cytometry assay methods to identifymammals having a latent tuberculosis infection (LTBI).

2. Background Information

Tuberculosis (TB) is important because it disproportionately affectsminorities and immigrants in the United States and vast populationsaround the world. Accurate detection of LTBI continues to bechallenging, and undiagnosed LTBI patients can progress to active TBdisease with potentially devastating consequences. Interpretation ofdiscordant testing (e.g., tuberculin skin tests (TST) andinterferon-gamma release assays (IGRA) in LTBI also can be a significantproblem. Both TST and IGRA tests usually detect T-cell activationagainst Mycobacterium tuberculosis (MTB), but they do not appear todifferentiate patients with dormant forms of TB infection from the oneswho have cleared their infections.

SUMMARY

This document provides methods and materials involved in performing flowcytometry assay methods. For example, this document provides flowcytometry assay methods and kits. In some cases, the methods and kitsprovided herein can be used to identify mammals having a LTBI.

As described herein, flow cytometry assay methods and kits can bedesigned to determine the percentage and/or number ofCD3⁻CD8⁺/CD25⁺/CD134⁻ cells present within a sample, the percentageand/or number of (CD3⁺)CD8⁺/CD25⁺/CD134⁺ cells present within a sample,and/or the percentage and/or number of (CD3⁺)CD4⁺/CD25⁺/CD134⁺ cellspresent within a sample. The flow cytometry assay methods and kitsprovided herein can identify highly likely LTBIs and subjects with priorexposure to TB that are falsely identified as being negative or falselyidentified as being positive with commercial assays such as QUANTIFERONTB GOLD IN-TUBE™ (Cellestis, Australia) and/or the tuberculin skin test(TST). The flow cytometry assay methods and kits provided herein canalso identify likely LTBIs that have a substantial risk of TBreactivation (“reactivatable LTBI”).

Having the ability to identify humans with a LTBI as described hereincan allow clinicians and other medical personnel to identify patients inneed of TB treatment in an accurate and efficient manner. In addition,the methods and materials provided herein can help the medical communitybetter target TB prevention strategies to those areas with cases ofLTBIs identified as described herein. In some cases, the methods andmaterials provided herein can be used to assist a qualified clinicianand/or healthcare provider in determining whether or not a mammal has alatent tuberculosis infection with or without substantial risk of TBreactivation.

In one aspect, this document features a flow cytometry assay method. Themethod can include (a) obtaining a sample comprising human cells, (b)exposing the human cells to an M. tuberculosis antigen preparation toobtain a stimulated human cell preparation, (c) contacting thestimulated human cell preparation with a fluorescently labeled anti-CD8antibody, a fluorescently labeled anti-CD25 antibody, and afluorescently labeled anti-CD134 antibody to obtain a labeled cellpreparation, and (d) introducing the labeled cell preparation into aflow cytometer to determine the percentage of CD8⁺/CD25⁺/CD134⁺ cellspresent within the labeled cell preparation. The human cells can behuman cells from a human having had a previous tuberculin skin test-(TST-) negative or interferon-gamma release assay- (IGRA-) negative testresult. The human cells can be human cells from a human having hadprevious TST-negative and IGRA− negative test results. The human cellscan be human cells from a human having had a previous TST-positive orIGRA-positive test result. The human cells can be human cells from ahuman having had a previous TST-positive and IGRA-positive test result.The human cells can be freshly obtained human cells, or can be frozenhuman cells. The human cells can be human peripheral blood mononuclearcells (PBMCs). The M. tuberculosis antigen preparation can include apolypeptide selected from the group consisting of ESAT-6₁₋₂₀,ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, and CFP-10₇₁₋₉₀polypeptides. The M. tuberculosis antigen preparation can containESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, andCFP-10₇₁₋₉₀ polypeptides. The method can include contacting thestimulated human cell preparation with a fluorescently labeled anti-CD4antibody. The percentage of CD4⁺/CD25⁺/CD134⁺ cells present within thelabeled cell preparation can be determined.

In another aspect, this document features a flow cytometry assay method.The method can include (a) obtaining a sample comprising human cells,(b) exposing the human cells to an M. tuberculosis antigen preparationto obtain a stimulated human cell preparation, (c) contacting thestimulated human cell preparation with a fluorescently labeled anti-CD3antibody, a fluorescently labeled anti-CD8 antibody, a fluorescentlylabeled anti-CD25 antibody, and a fluorescently labeled anti-CD134antibody to obtain a labeled cell preparation, and (d) introducing thelabeled cell preparation into a flow cytometer to determine thepercentage of CD3⁺/CD8⁺/CD25⁻/CD134⁻ cells present within the labeledcell preparation. The human cells can be human cells from a human havinghad a previous TST-negative or IGRA-negative test result. The humancells can be human cells from a human having had previous TST-negativeand IGRA-negative test results. The human cells can be human cells froma human having had a previous TST-positive or IGRA-positive test result.The human cells can be human cells from a human having had previousTST-positive and IGRA-positive test results. The human cells can befreshly obtained human cells, or can be frozen human cells. The humancells can be human PBMCs. The M. tuberculosis antigen preparation caninclude a polypeptide selected from the group consisting of ESAT-6₁₋₂₀,ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, and CFP-10₇₁₋₉₀polypeptides. The M. tuberculosis antigen preparation can containESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, andCFP-10₇₁₋₉₀ polypeptides. The method can include contacting thestimulated human cell preparation with a fluorescently labeled anti-CD4antibody. The percentage of CD3⁻/CD4⁻/CD25⁻/CD134⁺ cells present withinthe labeled cell preparation can be determined.

In another aspect, this document features a kit containing a M.tuberculosis antigen preparation, a fluorescently labeled anti-CD8antibody, a fluorescently labeled anti-CD25 antibody, and afluorescently labeled anti-CD134 antibody. The M. tuberculosis antigenpreparation can include a polypeptide selected from the group consistingof ESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, andCFP-10₇₁₋₉₀ polypeptides. The M. tuberculosis antigen preparation cancontain ESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀,and CFP-10₇₁₋₉₀ polypeptides. The kit can include a fluorescentlylabeled anti-CD4 antibody, or a fluorescently labeled anti-CD3 antibody.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 contains graphs plotting the lymphocyte proliferation assay (LPA)over time for cells from subjects with prior TST⁻ results, priorTST⁺/IGRA⁺ results, or prior TST⁺/IGRA⁻ results exposed to the indicatedantigens.

FIGS. 2A-2H contain examples of FACS-TB gating of quadrants forCD3⁺CD4⁺/CD25⁺/CD134⁺ T-cell subsets (right upper quadrant box in B andD-H) and controls. A-D) Viable lymphocyte gating strategy using side andforward scatter plots in PBMC stimulated with Staphylococcal enterotoxinA and B (SEAB) (A-B), and unstimulated sample (C-D); E-F) Isotypecontrols in SEAB-stimulated (E) and unstimulated samples (F); G) Singleanti-CD25⁺ fluorochrome staining in SEAB-stimulated sample; H) Singleanti-CD134⁺ fluorochrome staining in SEAB-stimulated sample.

FIGS. 3A-3H contain examples of FACS-TB test (% CD25⁺CD134⁺) gatingstrategy in activated T-cells (CD3⁺CD4⁺) in a suspected LTBI case (priorTST⁺/IGRA⁺ results). Only CD4⁺ T cells are shown (CD3⁺/CD4⁺ gated). A-B)Viable lymphocyte gate using side and forward scatter plots inSEAB-stimulated (A) and unstimulated (B) samples; C) Gate on CD3⁺/CD4⁺;D) % CD3⁺CD4⁺/CD25⁺CD134⁺ co-expression (right upper quadrant box) after48 hours incubation with SEAB (non-specific T-cell activator; positivecontrol); E) Unstimulated sample; F) PPD (non-specific MTB antigen); G)ESAT-6/CFP-10 peptide mixture (specific MTB antigen of RD1 (region ofdifference) peptide antigens); H) Candida (antigen-specific T-cellactivator; positive control). Percentages indicate the calculateddistribution of CD25⁺CD134⁺ among CD3⁺CD4⁺ T cells after the subtractionof background (nil).

FIGS. 4A-4H contain examples of FACS-TB test (% CD25+CD134+) gatingstrategy in activated T-cells (CD3+CD8+) in a suspected LTBI case (priorTST⁺/IGRA⁺ results). Only CD8⁺ T cells (CD8+high and CD8+low) are shown(CD3+/CD8+ gated). A-B) Viable lymphocyte gate using side and forwardscatter plots in SEAB-stimulated and unstimulated samples; C) Gate onCD3+/CD8+(high) and CD3+/CD8+(low); D) % CD3+CD8+(high andlow)/CD25+CD134+co-expression (right upper quadrant box) after 48 hoursincubation with SEAB (non-specific T-cell activator; positive control);E) Unstimulated sample; F) PPD (non-specific MTB antigen); G)ESAT-6/CFP-10 peptide mixture (specific MTB antigen of RD1 peptideantigens); H) Candida (antigen-specific T-cell activator; positivecontrol). Percentages (bold) indicate the calculated distribution ofCD25+CD134+ among CD3+CD8+ T cells after the subtraction of background(nil).

FIG. 5 contains graphs demonstrating FACS-TB reproducibility andcomparison between results using fresh and frozen peripheral bloodmononuclear cell samples for the indicated antigens.

FIG. 6 contains graphs demonstrating FACS-TB testing correlations.

FIG. 7 provides characteristics of the study population (N=33). ForeignHTB=foreign subject born in a high TB prevalence area; LTB=foreignsubject born in a low TB prevalence area.

FIG. 8 provides clinical characteristics of the study population (N=33).

FIG. 9 provides data for FACS-TB (RD1 and PPD) in CD4⁺ T-cells bycategory, including nonparametric statistical comparisons for each pairusing a Wilcoxon method (CD3⁺CD4⁺ T-cells activated by RD1 peptideantigens).

FIG. 10 contains graphs of FACS-TB (RD1) results in CD4⁺ T-cells forhealthy donors vs. LTBI cases (“Spec”=specificity; “Sens”=sensitivity).

FIG. 11 contains graphs of FACS-TB (RD1) results in CD4⁺ T-cells fordonors vs. TST+/IGRA+ (left panel) and TST+/IGRA− (right panel) cases.

FIG. 12 provides a summary of FACS-TB (RD1) results in CD4⁺ T-cells bycategory and TB contact likelihood.

FIG. 13 contains graphs of FACS-TB results in CD8⁺ T-cells (RD1 vs. PPD)by category.

FIG. 14 contains graphs of FACS-TB (RD1) results in CD8⁺ T-cells forhealthy donors vs. LTBI cases.

FIG. 15 contains graphs of FACS-TB (RD1) results in CD8⁺ T-cells fordonors vs. TST+/IGRA+ and TST+/IGRA− cases.

FIG. 16 contains a table of FACS-TB (RD1) results in CD4⁺ T-cells byTST/IGRA status.

FIG. 17 provides a summary of FACS-TB (PPD) results in CD4⁺ T-cells bycategory.

FIG. 18 provides a summary of FACS-TB (PPD) results in CD4⁺ T-cells fromhealthy donors vs. LTBI cases, including nonparametric statisticalcomparisons for each pair using a Wilcoxon method (CD3⁺CD4⁺ T-cellsactivated by PPD antigen).

FIG. 19 provides a summary of FACS-TB (PPD) results in CD4⁺ T-cells fromdonors vs. TST+/IGRA+ and TST+/IGRA− cases.

FIG. 20 contains a graph plotting FACS-TB (RD1) results in CD4⁺ T-cellsfrom unexposed donors (N=10) vs. untreated LTBI cases (N=14). (****)P<0.0001 (Mann-Whitney test). Dx=Diagnosis.

FIGS. 21A-21C contain graphs demonstrating the effect of isoniazidtreatment on FACS-TB (CD4⁺ T-cells; RD1 Ag) (A), TB-ELISPOT (RD1 Ag)(B), and QUANTIFERON-TB GOLD IN-TUBE™ (C) in LTBI cases. (A) LTBItreatment effect on FACS-TB in activated CD4⁺ T-cells (RD1-Ag-nil). (B)In-house ELISPOT (“TB-ELISPOT”) run with the same antigen stimulationconditions; and (C) QUANTIFERON TB GOLD IN-TUBE™; patients had adiagnosis of LTBI with a history of no treatment (“Untreated LTBI”;N=14), partial treatment (“Partially Treated LTBI”; N=3), or fulltreatment (“Treated LTBI”; N=7). Means (black lines). (**) P=0.002(Dunn's test). NS=no statistical significant differences. Tx=treatment.

FIG. 22 contains graphs demonstrating the effect of isoniazid treatmenton FACS-TB with RD1 peptides in CD4⁺ and FACS-TB with PPD in CD4⁺T-cells in LTBI cases. Patients had a history of untreated LTBI (“0”;N=14), partially treated LTBI (“1”; N=3) or treated LTBI (“2”; N=7).

FIG. 23 contains graphs demonstrating the effect of isoniazid treatmenton FACS-TB with PPD antigen in CD8⁺ (inclusive (high and low gate) andhigh gate) T-cells in LTBI cases. Patients had a history of untreatedLTBI (“0”; N=14), partially treated LTBI (“1”; N=3), or treated LTBI(“2”; N=7).

FIG. 24 contains graphs plotting FACS results for CD3⁻CD8⁺CD25⁺CD134⁻lymphocyte subsets activated by incubation with candida antigen (upperleft), SEAB superantigen (upper right), PPD antigen (lower left) and RD1peptide antigens (lower right) from healthy subjects with probable TBexposure (N=7), possible TB exposure (N=10), or no TB exposure (N=11),who have both negative QUANTIFERON TB GOLD IN-TUBE™ (Cellestis,Australia) and TST results.

DETAILED DESCRIPTION

This document provides methods and materials involved in performing flowcytometry assay methods. For example, this document provides flowcytometry assay methods and kits. In some cases, the methods and kitsprovided herein can be used to identify mammals (e.g., humans) having aLTBI.

A flow cytometry assay method provided herein can include incubatingcells (e.g., PBMCs or cells from a whole blood sample) with astimulation preparation. The cells can be freshly obtained cells orcells that have been stored or frozen. The stimulation preparation caninclude a mixture of ESAT-6 and CFP-10 polypeptides (RD1 peptideantigen). For example, a stimulation preparation can include a mixtureof ESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, andCFP-10₇₁₋₉₀ polypeptides. In some cases, a stimulation preparation caninclude a combination of an anti-CD28 antibody and an anti-CD49dantibody. Any appropriate length of time can be used for the incubationperiod. For example, the cells can be incubated as 37° C. for between 25and 90 hours (e.g., between 25 and 86 hours, between 25 and 60 hours, orbetween 35 and 45 hours).

Once the cells are treated with the stimulation preparation, they can bestained with fluorescently labeled antibodies. For example, the cells ofa stimulated cell preparation can be stained with fluorescently labeledanti-CD3 antibodies, fluorescently labeled anti-CD4 antibodies,fluorescently labeled anti-CD8 antibodies, fluorescently labeledanti-CD25 antibodies, fluorescently labeled anti-CD134 antibodies, or acombination thereof (e.g., a combination of fluorescently labeledanti-CD8 antibodies, fluorescently labeled anti-CD25 antibodies, andfluorescently labeled anti-CD134 antibodies). In some cases, the methodsprovided herein can be performed using unstimulated cells.

Once stained, the cells of the preparation can be subjected to flowcytometry to determine the percentage of CD3⁻CD8⁺/CD25⁺/CD134⁻ cellspresent within a sample, the percentage of (CD3⁺)CD8⁺7 CD25⁺/CD134⁺cells present within a sample, and/or the percentage of(CD3⁺)CD4⁺/CD25⁺/CD134⁺. In some cases, the number ofCD3⁻CD8⁺/CD25⁺/CD134⁻ cells, (CD3⁺)CD8⁺/CD25⁺/CD134⁺ cells, and/or(CD3⁺)CD4⁺/CD25⁺/CD134⁺ cells per a fixed number of cells (e.g., about2×10⁵ cells) can be determined. In some cases, the percentage ofCD8⁺/CD25⁺/CD134⁻ cells present within a sample, the percentage ofCD8⁺/CD25⁺/CD134⁺ cells present within a sample, the percentage ofCD4⁺/CD25⁺/CD134⁺, the number of CD8⁺/CD25⁺/CD134⁻ cells per a fixednumber of cells, CD8⁺/CD25⁺/CD134⁺ cells per a fixed number of cells,and/or CD4⁺/CD25⁺/CD134⁺ cells per a fixed number of cells can be usedto determine if a mammal has a LTBI. In some cases, a percentage of(CD3⁺)CD8⁺/CD25⁺/CD134⁺ of antigen-specific activated cells presentwithin a sample that is greater than 0.12% (RD1 antigen minus nil)and/or 0.11% (PPD antigen minus nil) can indicate that the mammal has aLTBI with reactivation potential. In some cases, a percentage of(CD3⁺)CD4⁺/CD25⁺/CD134⁺ of antigen-specific activated cells presentwithin a sample that is greater than 0.002% (RD1 antigen minus nil) and0.39% (PPD antigen minus nil) can indicate that the mammal has a LTBIwith reactivation potential. In some cases, a percentage of(CD3+)CD4+/CD25+/CD134+ of antigen-specific activated cells presentwithin a sample that is greater than 0.04% (RD1 antigen minus nil) and0.39% (PPD antigen minus nil) can indicate that the mammal has a LTBIwith reactivation potential. In some cases, a number ofCD3⁻CD8⁺/CD25⁺/CD134⁻ of antigen-specific activated cells greater than 6(RD1 antigen minus nil) and/or 27 (PPD antigen minus nil) per 2×10⁵cells can indicate that the mammal has had an exposure to TB without anapparent adaptive T-cell response to TB. In some cases, a number of(CD3⁺)CD8⁺/CD25⁺/CD134⁺ of antigen-specific activated cells greater than9 (PPD antigen minus nil) per 2×10⁵ cells can indicate that the mammalhas a LTBI with reactivation potential. In some cases, a number of(CD3⁺)CD4⁺/CD25⁺/CD134⁺ of antigen-specific activated cells greater than10 (RD1 antigen minus nil) and/or 70 (PPD antigen minus nil) per 2×10⁵cells can indicate that the mammal has a LTBI with reactivationpotential.

In some cases, background counts such as the number of (CD3⁺)CD4⁺ (orCD8⁺)/CD25⁺/CD134⁺ cells found in unstimulated samples (nil or mediawithout antigen(s)) can be subtracted prior to assessing whether or nota mammal has a LTBI. For example, a number of (CD3⁺)CD8⁺/CD25⁺/CD134⁺ ofantigen-specific activated cells greater than 8 (RD1 antigen minus nil)and/or 9 (PPD antigen minus nil) per 2×10⁵ cells can indicate that themammal has a LTBI with reactivation potential. Likewise, a number of(CD3⁺)CD4⁺/CD25⁺/CD134⁺ of antigen-specific activated cells greater than10 (RD1 antigen minus nil) and/or 70 (PPD antigen minus nil) per 2×10⁵cells can indicate that the mammal has a LTBI with reactivationpotential.

This document also provides kits for performing a flow cytometry assaymethod provided herein. For example, reagents of a stimulationpreparation and reagents for assessing cells for expression of CD3, CD4,CD8, CD25, and/or CD134 can be combined as an article of manufacturesuch as a kit. In one embodiment, a kit can contain an M. tuberculosisantigen preparation such as a mixture of ESAT-6 and CFP-10 polypeptidesfor stimulating cells and fluorescently labeled anti-CD3 antibodies,fluorescently labeled anti-CD4 antibodies, fluorescently labeledanti-CD8 antibodies, fluorescently labeled anti-CD25 antibodies,fluorescently labeled anti-CD134 antibodies, or a combination thereof(e.g., a combination of fluorescently labeled anti-CD8 antibodies,fluorescently labeled anti-CD25 antibodies, and fluorescently labeledanti-CD134 antibodies). In some case, a kit provided herein can includean anti-CD28 antibody and/or an anti-CD49d antibody in addition to an M.tuberculosis antigen preparation and control samples for stimulatingcells and unstimulated cells.

In some cases, a kit can contain buffers, positive control samples, orcombinations thereof. The reagents within a kit can be housed togetherin various combinations or can be packaged in separate vials orcontainers within a larger package. The kits provided herein also caninclude labels or packaging inserts setting out instructions forpreparation and use. For example, a kit can contain a packaging insertdescribing that an elevated level of CD8⁺/CD25⁺/CD134⁺ cells can supporta diagnosis of LTBI.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

Examples Example 1—Evaluation of a Flow Cytometric Method for theDiagnosis of Latent Tuberculosis Infection

The following was performed to evaluate the diagnostic performance of aFACS assay for the detection of T-cell CD25⁺CD134⁺ co-expression(FACS-TB) in healthy subjects and suspected LTBI cases. A prospectivecomparison of the diagnostic characteristics of FACS-TB using peripheralblood mononuclear cells (PBMCs) samples from subjects unlikely to haveLTBI (low probability of previous TB contact and both negative TST andcommercial IGRA) and likely to have LTBI (high probability of TB contactand/or both TST+/IGRA+ tests) was performed. PBMCs were stimulated withspecific (RD1-peptides) and non-specific (PPD) MTB antigens as well ascontrols, stained with fluorescent dye-conjugated anti-CD4, anti-CD25,and anti-OX40 (anti-CD134) antibodies, and 2×10⁵ cells were analyzed byFACS (BD FACSCanto™). The area under the receiver characteristic (ROC)curve (AUC) were analyzed, and various cut-offs to best differentiatethese populations were tested.

The FACS-TB assay protocol was developed to detect LTBIs. The followingsteps 1 and 2 were performed on day 1, and the following steps 3 through11 were performed on day 3.

1. Prepare cell culture media: Use a conical tube; add 50 mL RPMI 1640(with 2 mM L-glutamine) supplemented with 10% human AB serum and 0.5 mLof Pen-Strep mixture (Gibco #15140-122) to final concentration ofpenicillin 100 IU/mL and streptomycin (100 μg/mL) in culture medium.

2. Within 2 hours of blood collection in heparinized tubes (total 20 ccor less for fresh whole blood), harvest peripheral blood monocytes(PBMC) using a density gradient centrifugation of whole blood(Ficoll-Plaque™ technique), wash cells two times with PBS and add cellculture media in a polypropylene sterile tube for a final concentration2.5×10⁶ PBMCs/mL. Harvest cells can be used directly in assay or freezeusing RPMI with 10% DMSO and 12% Human Sera Albumin or FBS. Immediatelyafter putting cells in cryovials, put in the freezer at −80° C. and/orliquid nitrogen. Frozen cell pellets can be sent in mail package withdry ice for subsequent laboratory processing after thawing.

3. Perform stimulation procedures with PBMC's using concentration of (a)Staphylococcus Enterotoxin A and B (SEAB) or other super antigen ormitogen (e.g., phytohemagglutinin (PHA), anti-CD3 monoclonalantibodies), (b) tuberculin PPD™ (Staten Serum Institute, Denmark), (c)RD1-peptide mix (ESAT-6 and CFP-10 peptides mix), or (d) Candida proteinmix. An unstimulated sample is used as a control. Four ESAT-6polypeptides and two CFP-10 polypeptides are included in the RD1-peptidemix. The ESAT-6 polypeptides are ESAT-6₁₋₂₀ (MTEQQWNFAGIEAAASAIQG; SEQID NO:1), ESAT-6₃₁₋₅₀ (EGKQSLTKLAAAWGGSGSEA; SEQ ID NO:2), ESAT-6₄₂₋₆₅(AWGGSGSEAY-QGVQQKWDATATEL; SEQ ID NO:3), and ESAT-6₆₁₋₈₀(TATELNNALQNLARTIS-EAG SEQ ID NO:4). The CFP-10 polypeptides areCFP-10₅₁₋₇₀ (AQAAVVRFQEA-ANKQKQELD; SEQ ID NO:5) and CFP-10₇₁₋₉₀(EISTNIRQAGVQYSRADEEQ; SEQ ID NO:6).

4. Keep 2.5 mL of blood sample for whole blood experiments using thefollowing antigen stimulation conditions and controls.

5. Stimulation procedure (under the hood):

-   -   a. Tube 1 (SEAB to final concentration at 2 ng/mL w/v same final        concentration as per PMBC's stimulation conditions):        -   i. Dilute 24 μL of freshly thawed SEAB stock (0.5 ng/μL) and            in 476 μL of culture media.        -   ii. Then add 3 mL of diluted fresh SEAB to 3 mL of whole            blood from Sodium heparin sample to tube 1 (total of 3 mL).    -   b. Tube 2 (PPD final concentration of 20 μg/mL—same final        concentration as per PMBCs stimulation conditions):        -   i. Tube 2: “PPD”: Add 60 μL of PPD in 1.44 mL of culture            media.        -   ii. Then add 1.5 mL of diluted PPD and 1.5 mL of whole blood            from Sodium heparin sample to tube 2 (“PPD at 20 μg/mL”) (3            mL total).    -   c. Tube 3 (CFP-10+ESAT-6 peptide mix same final concentrations        per PMBC's stimulation conditions):        -   i. Tube 3: “CFP-10 (add at 4 μg/mL)/ESAT-6 mix (add at 2            μg/mL)”: all stock is 1 μg/μ.L. Add 12 μL of CFP10 and add 6            μL of ESAT-6 with 1.49 mL of culture media.        -   ii. Add 1.5 mL of diluted fresh CFP-10/ESAT-6 in culture            media at 1.5 mL of whole blood from sodium heparin sample to            tube: (3 mL total).    -   d. Tube 4 (Candida activated same final concentration as per        PMBC's stimulation conditions):        -   i. Dilute 3 μL of Candida stock solution (10 μg/μL) in 1.5            mL of culture media (“Candida to 10 μg/mL in culture            media”).        -   ii. Then add 1.5 mL of diluted Candida and 1.5 mL of whole            blood from Sodium heparin sample to tube (3 mL total).

6. Tube 5 (“unstimulated blood”):

-   -   a. Use 1.5 mL of whole blood from Sodium heparin sample for tube        5, then add 1.5 mL of culture medium to dilute 1:1.

7. Add 5 μL of anti-CD28/anti-CD49d reagent (Becton DickinsonFastImmune™ CD28/CD49d Costimulatory Reagent; BD Biosciences cat#347690)to activated tubes (Tubes 2, 3, 4, and 5) and vortex gently.

8. Incubate all tubes in a CO₂ incubator at 37° C. for about 40 hours.

9. Incubated tubes are stained with fluorescent dye-conjugated anti-CD3,anti-CD4 (or antiCD8), anti-CD25, and anti-OX40 (anti-CD134) antibodies,and 2×10⁵ cells were analyzed by FACS (BD FACSCanto™)

10. Set FACS-TB gating of quadrants for CD3⁺CD4⁺ (or CD8⁺)/CD25⁺/CD134⁺T-cell subsets (Please see example in FIG. 2) and controls by usingFloJow™ or similar software. Gate for viable lymphocytes by using sideand forward scatter plots in PBMC stimulated with Staphylococcalenterotoxin A and B (SEAB), and unstimulated sample. Gate upper rightquadrant quadrants for CD3⁺CD4⁺/CD25⁺/CD134⁺ T-cell subsets by usingisotype controls in SEAB-stimulated and unstimulated samples. Confirmquadrants for CD3⁺CD4⁺/CD25⁺/CD134⁺ T-cell subsets by gating a singleanti-CD25⁺ fluorochrome staining in a SEAB-stimulated sample, and asingle anti-CD134⁺ fluorochrome staining in a SEAB-stimulated sample.

11. Set FACS-TB test gating (% CD25⁺CD134⁺) in activated T-cells(CD3⁺CD4⁺ (or CD8⁺)) (Please see FIGS. 3 and 4). Gate for viablelymphocytes by using side and forward scatter plots in SEAB-stimulatedand unstimulated samples. Gate on CD3⁺/CD4⁺; D) % CD3⁺CD4⁺/CD25⁺CD134⁺co-expression (right upper quadrant box set from prior step) with SEAB(non-specific T-cell activator; positive control), unstimulated sample(negative or nil control), PPD (non-specific MTB antigen), ESAT-6/CFP-10peptide mixture (specific MTB antigen of RD1(region of difference)peptide antigens) and Candida (antigen-specific T-cell activator;positive control). Percentages (or numbers) indicate the calculateddistribution of CD25⁺CD134⁺ among CD3⁺(or CD3⁻)CD4⁺ (or CD8⁺) cellsafter the subtraction of background (nil).

Thirty-three consecutive subjects, including 17 healthy donors withTST−/IGRA− results, 9 patients with TST+/IGRA+ results (8 with probableTB exposure and 1 close contact), 2 with recently diagnosed active TB, 3patients with TST+/IGRA− results (2 with probable TB exposure and 1 withpossible TB exposure), and 2 with remotely treated TB (one with IGRA−results) were analyzed. Statistically significant differences in FACS-TBresults were found between healthy donors and suspected LTBI cases(P<0.001). FACS-TB for CD4⁺ T-cells AUC of ROC was 0.97; sensitivity of100.0% and specificity of 88% at the best cut off of 0.07% of T-cellsfor clinical diagnosis of LTBI with TST+/IGRA+ results. In addition, anincreased number of activated CD8⁺ T-cells with CD25⁺/CD134⁺co-expression was found not only in a case of disseminated TB but alsoin a subset of LTBI cases. Additional results are provided in FIGS.1-19.

The FACS-TB testing of CD4⁺ T-cells revealed a high diagnostic yield forLTBI in this patient population.

Example 2—Treatment Effect of Isoniazid on T-Cell CD25⁺/CD134⁺Co-Expression in Latent Tuberculosis Infection

The following was performed to evaluate flow cytometric detection ofantigen-specific activated T-cell CD25⁺CD134⁺ co-expression in highlysuspected LTBI subjects with a history of no treatment or treatment withisoniazid. Flow cytometric detection of CD25⁺CD134⁺ co-expression onantigen-stimulated T-cells was performed using peripheral bloodmononuclear cells (PBMCs) samples from subjects likely to have LTBI(risk factors for TB and TST+/IGRA+ tests or TST conversion) and havinga history of no treatment partial treatment, or complete isoniazidtreatment. PBMCs were stimulated with specific (RD1-peptides),non-specific (PPD) MTB antigens, or controls, stained with fluorescentdye-conjugated anti-CD3, anti-CD4, anti-CD25, and anti-OX40 antibodies,and 2×10⁵ cells were analyzed by FACS. The percentages of CD3⁺CD4⁺T-cells co-expressing CD25 and CD134 in these three populations werecompared.

Fourteen highly suspected LTBI subjects naïve to treatment, threesubjects partially treated with isoniazid, and nine subjects with priorcompletion of LTBI therapy were studied. Statistically significantreductions in CD25⁺CD134⁺ co-expression in antigen-stimulated T-cells inpatients with prior LTBI treatment (P<0.05) were observed. There were nostatistical differences in QUANTIFERON TB GOLD IN-TUBE™ results and anELISPOT run under the same antigen stimulation conditions. Additionalresults are provided in FIGS. 20-23.

These results demonstrate that a FACS assay can detect LTBI withreactivation potential. For example, these results demonstrate that anex vivo FACS method with CD3+CD4+ and CD3+CD8+ T-cells with eitherRD1-peptides or PPD antigens have a high diagnostic accuracy to detectsuspected LTBI cases, that a FACS method with CD3+CD4+ T-cells witheither RD1-peptides or PPD can detect suspected LTBI cases withreactivation potential (e.g., high reactivation potential; reactivatableLTBI), and that a FACS method with CD3+CD8+ T-cells with PPD antigen candetect suspected LTBI cases with reactivation potential (e.g., highreactivation potential; reactivatable LTBI).

Example 3—Flow Cytometric Approach to Evaluate Innate Immunity inSubjects Exposed to TB with Negative TST and IGRA Results

The following was performed to evaluate the flow cytometric detection ofCD3⁻CD8⁻CD25^(−P)CD134⁻ cells in response to MTB antigens in healthysubjects with negative Tuberculin skin test (TST) and Interferon-γrelease assay (IGRA) and various likelihood of prior TB exposures. Aprospective evaluation of FACS detection of CD3⁻CD8⁺CD25⁺CD134⁻ cells inresponse to MTB antigens was performed using peripheral bloodmononuclear cells (PBMCs) samples from healthy subjects with unlikely,possible, and probable prior TB exposure and negative TST and IGRAresults. PBMCs were stimulated with specific (RD1-peptides) andnon-specific (PPD) MTB antigens as well as controls, stained withfluorescent dye-conjugated anti-CD3, anti-CD8, anti-CD25, and anti-OX40(anti-CD134) antibodies, and 2×10⁵ cells were analyzed by FACS (BDFACSCANTO™). The area under the receiver characteristic (ROC) curve(AUC) was analyzed, and various cut-offs were tested to bestdifferentiate these populations.

Twenty-eight consecutive subjects, including 11 healthy donors born inthe US and with unlikely prior TB exposure; 10 subjects with possible TBexposure (being born in and nonmedical trips to moderate to high TBprevalence areas (HTA)), and 7 subjects with prior close contact withactive TB patients in HTA and with TST−/IGRA− results were analyzed.Statistically significant differences in number of CD3⁻CD8⁺CD25⁺CD134⁻cells in response to PPD (P=0.017) and RD1-peptide antigens (P=0.028)between subjects with unlikely and probable prior TB exposure wereobserved (FIG. 24). No significant differences were found in these PBMCsubsets stimulated to candida and staphylococcal enterotoxin A and Bantigens (FIG. 24) with any of these antigens, potentially suggesting abiomarker candidate of innate immunity.

These results suggest that flow cytometric detection ofCD3⁻CD8⁺CD25⁺CD134⁻ cells in response to MTB antigens can detect innateimmune recall response to prior TB exposures in subjects withoutadaptive immune response to MTB antigens.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A kit comprising a M. tuberculosis antigenpreparation, a fluorescently labeled anti-CD8 antibody, a fluorescentlylabeled anti-CD25 antibody, and a fluorescently labeled anti-CD134antibody.
 2. The kit of claim 1, wherein said M. tuberculosis antigenpreparation comprises a polypeptide selected from the group consistingof ESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀, ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CEP-10₅₁₋₇₀, andCFP-10₇₁₋₉₀ polypeptides.
 3. The kit of claim 1, wherein said M.tuberculosis antigen preparation comprises ESAT-6₁₋₂₀, ESAT-6₃₁₋₅₀,ESAT-6₄₂₋₆₅, ESAT-6₆₁₋₈₀, CFP-10₅₁₋₇₀, and CFP-10₇₁₋₉₀ polypeptides. 4.The kit of claim 1, wherein said kit comprises a fluorescently labeledanti-CD4 antibody.
 5. The kit of claim 1, wherein said kit comprises afluorescently labeled anti-CD3 antibody.